Hi. On Fri, Apr 22, 2011 at 1:30 PM, HWright <wrig...@ohsu.edu> wrote: > Hello; I'm quite new to analysis of the CNV/SNP chips and totally new > to AROMA, so I apologize if this is an obvious question, but I'm > attempting to use AROMA to step through the CRLMM genotyping vignette > on some 6.0 chips we have and am encountering the following error > after the SNPRMA normalization: > > Error in list(`CrlmmModel(ces, tags = "*,oligo")` = <environment>, > `throw("Cannot fit CRLMM model: Chip type to be supported: ", > chipType)` = <environment>, : > > [2011-04-22 13:12:55] Exception: Cannot fit CRLMM model: Chip type to > be supported: GenomeWideSNP_6
Unfortunately, fitting/running CRLMM in aroma.affymetrix on GenomeWideSNP_6 is not supported/implemented. > > Are the 6.0s not supported for this in Affy? Do I need to use oligo to > do this? Yes, you need to use the oligo package for running CRLMM on GenomeWideSNP_6. > Is this unnecessary and all this information would come out > of a CRMA/ACNE analysis (we would like to get copy number as well for > our analysis)? If you want to do copy number analysis, I recommend that you use the CRMAv2 preprocessing method which will give you locus-by-locus copy-number estimates, which you then can pass on to segmentation methods such as CBS. All this can be done within the aroma framework. If you want *genotype calls* for your GenomeWideSNP_6, you need to use oligo or another genotyping software. Note that genotype calls per se are not needed for doing copy-number analysis/inference. > I searched the group archives but most of the posts > were from 2008 regarding not supporting CRLMM and since there was a > vignette (albeit for 100k/500k) I wasn't sure if that was still the > case. Yes, that is still the case. Hope this helps Henrik > Thanks... > > Hollis > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/